Variant report

Variant	rs6492825
Chromosome Location	chr13:96570980-96570981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 134 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:128)

rs_ID	r²[population]
rs1015068	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11070154	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11070157	0.82[AMR][1000 genomes]
rs1114308	0.82[AMR][1000 genomes]
rs11616658	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11619333	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11619490	0.80[AMR][1000 genomes]
rs11839843	0.81[EUR][1000 genomes]
rs11840966	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11841021	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11842396	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12858210	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12870771	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12876018	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1411557	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1537030	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1537031	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17189895	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17189951	0.81[AMR][1000 genomes]
rs1813179	0.80[AMR][1000 genomes]
rs1872161	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2026819	0.82[AMR][1000 genomes]
rs2062276	0.82[AMR][1000 genomes]
rs2129005	0.80[AMR][1000 genomes]
rs2170812	0.80[AMR][1000 genomes]
rs2389532	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2389570	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2389571	0.80[AMR][1000 genomes]
rs28649586	0.82[AMR][1000 genomes]
rs34738594	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34816227	0.80[AMR][1000 genomes]
rs35423192	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35836619	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35898412	0.82[AMR][1000 genomes]
rs36079088	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs36101002	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3782989	0.81[AMR][1000 genomes]
rs3825424	0.81[AMR][1000 genomes]
rs4547218	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4771923	0.82[AMR][1000 genomes]
rs4773928	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4773929	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4773933	0.80[AMR][1000 genomes]
rs4773934	0.80[AMR][1000 genomes]
rs55822301	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56322430	0.81[EUR][1000 genomes]
rs57924129	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59592654	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60677558	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61972920	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492824	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6492827	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67447270	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7317285	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7321296	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7322566	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7323150	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7323734	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7323780	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7324957	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7325690	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7325915	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7327532	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7328703	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7331461	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7331926	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332683	0.80[AMR][1000 genomes]
rs7333370	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7333843	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7334100	0.81[AMR][1000 genomes]
rs7335319	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7335514	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7336088	0.80[ASN][1000 genomes]
rs7336373	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7337653	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7338224	0.82[AMR][1000 genomes]
rs7338859	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs764714	0.80[AMR][1000 genomes]
rs7981923	0.83[EUR][1000 genomes]
rs7982337	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7983546	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7984584	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7986005	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7992875	0.80[AMR][1000 genomes]
rs7998353	0.82[AMR][1000 genomes]
rs8000849	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8002064	0.83[EUR][1000 genomes]
rs9556502	0.83[EUR][1000 genomes]
rs9556503	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9556504	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9556505	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9556506	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9556508	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9556509	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9556511	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9556512	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9556513	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9556515	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9556518	0.82[AMR][1000 genomes]
rs9556520	0.82[AMR][1000 genomes]
rs9556523	0.80[AMR][1000 genomes]
rs9561964	0.83[EUR][1000 genomes]
rs9561967	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9561969	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9561971	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9561973	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9561974	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9561975	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9561976	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9561981	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9561984	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9561985	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9561987	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9561988	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9561991	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9561995	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9561996	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9561998	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9562003	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9562005	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs9562006	0.91[ASN][1000 genomes]
rs9562007	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9562008	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9562012	0.82[AMR][1000 genomes]
rs9562015	0.82[AMR][1000 genomes]
rs9562016	0.82[AMR][1000 genomes]
rs9562018	0.80[AMR][1000 genomes]
rs9670470	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832691	chr13:96478098-96659823	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv900935	chr13:96497070-96631221	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv1050430	chr13:96508530-97020734	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv541883	chr13:96508530-97020734	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
5	nsv1041165	chr13:96522021-96966520	Enhancers Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1051574	chr13:96550653-96779248	Strong transcription Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6492825	DNAJC3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96495000-96590800	Weak transcription	Rectal Smooth Muscle	rectum
2	chr13:96503400-96580800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr13:96523200-96581800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr13:96536200-96587200	Weak transcription	Stomach Smooth Muscle	stomach
5	chr13:96542400-96576800	Weak transcription	HSMMtube	muscle
6	chr13:96542400-96581600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr13:96543000-96581600	Weak transcription	Fetal Lung	lung
8	chr13:96543000-96581800	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr13:96543000-96586800	Weak transcription	Brain Hippocampus Middle	brain
10	chr13:96543400-96576600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr13:96544600-96576800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr13:96549400-96586400	Weak transcription	Hela-S3	cervix
13	chr13:96553200-96573600	Weak transcription	Osteobl	bone
14	chr13:96558400-96586600	Weak transcription	Right Ventricle	heart
15	chr13:96558600-96579000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr13:96559600-96576600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:96559600-96576800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr13:96559600-96580800	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr13:96559600-96583000	Weak transcription	Pancreas	Pancrea
20	chr13:96559600-96586400	Weak transcription	A549	lung
21	chr13:96559800-96580600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr13:96559800-96580600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr13:96559800-96583400	Weak transcription	Esophagus	oesophagus
24	chr13:96559800-96588600	Weak transcription	Gastric	stomach
25	chr13:96560000-96572000	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr13:96560000-96581400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr13:96560000-96581600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr13:96560200-96581000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr13:96562600-96580600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr13:96566200-96576800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr13:96566400-96573200	Weak transcription	Brain Germinal Matrix	brain
32	chr13:96566400-96576200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:96566400-96581600	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr13:96566800-96587000	Weak transcription	Colon Smooth Muscle	Colon
35	chr13:96567600-96575400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr13:96567600-96581600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr13:96568200-96576600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr13:96568200-96576800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr13:96568200-96578400	Weak transcription	Fetal Kidney	kidney
40	chr13:96568400-96576400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr13:96568400-96577400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr13:96568400-96579600	Weak transcription	GM12878-XiMat	blood
43	chr13:96568400-96580600	Weak transcription	Fetal Intestine Large	intestine
44	chr13:96568400-96581600	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr13:96568600-96571200	Weak transcription	Fetal Intestine Small	intestine
46	chr13:96568600-96576800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr13:96568600-96576800	Weak transcription	Fetal Muscle Leg	muscle
48	chr13:96568600-96577000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr13:96568600-96577400	Weak transcription	Adipose Nuclei	Adipose
50	chr13:96568600-96580600	Weak transcription	Fetal Muscle Trunk	muscle

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